Genomic anatomy of the specific reciprocal translocation t(15;17) in acute promyelocytic leukemia

Abstract

The genomic breakpoints in the t(15;17)(q22;q21), associated with acute promyelocytic leukemia (APL), are known to occur within three different PML breakpoint cluster regions (bcr) on chromosome 15 and within RARA intron 2 on chromosome 17; however, the precise mechanism by which this translocation arises is unclear. To clarify this mechanism, we (i). assembled the sequence of RARA intron 2, (ii). amplified and sequenced the genomic PML-RARA junction sequences from 37 APL patients, and (iii). amplified and sequenced the reverse RARA-PML genomic fusion in 29 of these cases. Three significant breakpoint microclusters within RARA intron 2 were identified, suggesting that sequence-associated or structural factors play a role in the formation of the t(15;17). There was no evidence that the location of a breakpoint in PML had any relationship to the location of the corresponding breakpoint in RARA. Although some sequence motifs previously implicated in illegitimate recombinations were found in the microcluster regions, these associations were not significant. Comparison of forward and reverse genomic junctions revealed microhomologies, deletions, and/or duplications of either gene in all but one case, in which a complex rearrangement with inversion of the PML-derived sequence was found. These findings are consistent with the hypothesis that the t(15;17) occurs by nonhomologous recombination of DNA after processing of the double-strand breaks by a dysfunctional DNA damage-repair mechanism.

Standardization and quality control studies of ‘real-time’ quantitative reverse transcriptase polymerase chain reaction of fusion gene transcripts for residual disease detection in leukemia – A Europe Against Cancer Program

“…It should be noted that the size of the PCR products varies in bcr2-positive cases, because of the variable breakpoint positions in exon 6 of the PML gene and inclusion of a variable number of RARA intron 2-derived nucleotides in the FG transcript. 156 Chimeric PML-RARA and RARA-PML transcripts are formed as a consequence of the reciprocal translocation between the PML and RARA loci. However, the observation that RARA-PML FG transcripts are present in most but not all APL cases, has favored the use of PML-RARA FG transcripts as PCR target for detection of APL cells at diagnosis and during monitoring.…”

Acute promyelocytic leukemia: where does it stem from?

“…Characterization of genomic breakpoints in patients with APL has revealed a complex pattern with microhomologies, deletions and inversions suggesting that the t(15;17) is likely to arise as a result of double-strand DNA breakage followed by nonhomologous end-joining. 16,17 However, an important issue that remains to be resolved is the nature of the hematopoietic progenitor that is the normal target of the PML-RARa fusion in this disease. In this review, we consider the pertinent experimental evidence to date, particularly with respect to different neoplastic conditions and its implications for the origin of APL.…”

Analysis of genomic breakpoints in p190 and p210 BCR–ABL indicate distinct mechanisms of formation

“…Sequence analysis of myeloid translocation breakpoints has revealed that the majority probably result from NHEJ following DNA breakage, 4,33,38,39 however, the reason why some fusions are seen very frequently compared with other known or potential fusions is still unclear. By contrast, the mechanisms giving rise to many chromosomal translocations in lymphoid malignancies are believed to be the result of illegitimate lymphoid-specific recombination mechanisms, such as V(D)J 16,34,40,41 or class switch recombination.…”

“…3 Analysis to date has indicated that translocations in leukemia result from non-homologous end joining (NHEJ) following two double stranded DNA breaks; homologous recombination does not have a significant role. 4,5 The paradigm for translocations in leukemia is the Philadelphia (Ph) chromosome, the smaller derivative of the t(9;22). 6 The resultant BCR-ABL fusion gene is the defining marker of chronic myeloid leukemia (CML).…”